Gene Expression in Yeasts During Wine Fermentation

Bisson, Linda F.

doi:10.1007/978-1-4939-9782-4_5

Cited by 6 publications

(8 citation statements)

References 208 publications

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“…These processes, coupled with enrichment of associated pathways involved in RNA transcription and transport, reflect energy use for cell growth and proliferation associated with log phase growth occurring in early fermentation. Further in fermentation, changes in ribosomal machinery gene expression occurred, as reported in previous studies(49) (Figure 2C), reflecting a transition to a non-proliferative metabolic state. Late in fermentation this was accompanied by changes in gene expression linked to nutrient limitation, altered metabolism, and entry into meiosis (Figures 2C and S3-S4), which included gene expression patterns consistent with hallmark isoform switches in hexose transporters and glycolytic enzymes that occur as concentrations of glucose or fructose change(50)…”

supporting

confidence: 81%

“…As ethanol concentrations rise through the end of fermentation, a gradual transcriptome response to ethanol stress is also observed (3). This response overlaps with, but appears distinct from, the environmental stress response seen in laboratory yeast (2,3,7), which may be related to the multitude of simultaneous stresses experienced by the yeast at the end of a wine fermentation (Bisson 2019). Indeed, the majority of genes with stress response elements in their promoter are expressed at the end of fermentation (8).…”

Section: Introductionmentioning

confidence: 86%

“…and PHO89 are phosphate transporters that are induced during phosphate starvation (52), both of which are expressed in early fermentation, along with PHO90. Phosphate limitation can cause stuck fermentations, as phosphate is critical for cellular function as a component of ATP, nucleotides, sugars, lipids, and macromolecules such as proteins (49,53). Given that all these Pinot noir fermentations went to completion, and that the majority of glucose was converted to ethanol after the 16hrs time point, induction of genes encoding phosphate transporters early in fermentation is not likely associated with phosphate starvation.…”

Section: Nutrient Limitation In Early Fermentationmentioning

confidence: 99%

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Saccharomyces cerevisiaegene expression during fermentation of Pinot noir wines at industrially relevant scale

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Montpetit

Byer

et al. 2021

Preprint

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During a wine fermentation, Saccharomyces cerevisiae transforms grape must through metabolic activities that generate ethanol and other compounds. Thousands of genes change expression over the course of a wine fermentation to allow S. cerevisiae to adapt to and dominate the fermentation environment. Investigations into these gene expression patterns have previously revealed genes that underlie cellular adaptation to the grape must and wine environment involving metabolic specialization and ethanol tolerance. However, the vast majority of studies detailing gene expression patterns have occurred in controlled environments that do not recapitulate the biological and chemical complexity of fermentations performed at production scale. Here, we present an analysis of the S. cerevisiae RC212 gene expression program across 40 pilot-scale fermentations (150 liters) using Pinot noir grapes from 10 California vineyards across two vintages. We observe a core gene expression program across all fermentations irrespective of vintage similar to that of laboratory fermentations, in addition to novel gene expression patterns likely related to the presence of non-Saccharomyces microorganisms and oxygen availability during fermentation. These gene expression patterns, both common and diverse, provide insight into Saccharomyces cerevisiae biology critical to fermentation outcomes at industry-relevant scales.ImportanceThis study characterized Saccharomyces cerevisiae RC212 gene expression during Pinot noir fermentation at pilot scale (150 liters) using production-relevant conditions. The reported gene expression patterns of RC212 is generally similar to that observed in laboratory fermentation conditions, but also contains gene expression signatures related to yeast-environment interactions found in a production setting (e.g., presence of non-Saccharomyces microorganisms). Key genes and pathways highlighted by this work remain under-characterized, raising the need for further research to understand the roles of these genes and their impact on industrial wine fermentation outcomes.

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supporting

confidence: 81%

Section: Introductionmentioning

confidence: 86%

Section: Nutrient Limitation In Early Fermentationmentioning

confidence: 99%

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Saccharomyces cerevisiaegene expression during fermentation of Pinot noir wines at industrially relevant scale

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Montpetit

Byer

et al. 2021

Preprint

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“…For example, in experiments that study the cell cycle, inhibitors arrest the cell cycle at the same stage across groups thereby enabling comparisons (24). This experimental approach is not applicable to wine fermentations where nutrient availability is more important than stage of the cell cycle (25).…”

Section: Introductionmentioning

confidence: 99%

Mapping global shifts inSaccharomyces cerevisiaegene expression across asynchronous time trajectories with diffusion maps

Reiter

Montpetit

Runnebaum

et al. 2021

Preprint

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Grapes grown in a particular geographic region often produce wines with consistent characteristics, suggesting there are site-specific factors driving recurrent fermentation outcomes. However, our understanding of the relationship between site-specific factors, microbial metabolism, and wine fermentation outcomes are not well understood. Here, we used differences in Saccharomyces cerevisiae gene expression as a biosensor for differences among Pinot noir fermentations from 15 vineyard sites. We profiled time series gene expression patterns of primary fermentations, but fermentations proceeded at different rates, making analyzes of these data with conventional differential expression tools difficult. This led us to develop a novel approach that combines diffusion mapping with continuous differential expression analysis. Using this method, we identified vineyard specific deviations in gene expression, including changes in gene expression correlated with the activity of the non-Saccharomyces yeastHanseniaspora uvarum, as well as with initial nitrogen concentrations in grape musts. These results highlight novel relationships between site-specific variables and Saccharomyces cerevisiae gene expression that are linked to repeated wine fermentation outcomes. In addition, we demonstrate that our analysis approach can extract biologically relevant gene expression patterns in other contexts (e.g., hypoxic response of Saccharomyces cerevisiae), indicating that this approach offers a general method for investigating asynchronous time series gene expression data.

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“…The volatile metabolic profile obtained during fermentation of different carbohydrates is reflective of the raw ingredients composition [37,38]. Wine is perhaps one of the oldest biotechnologies as yeast are often found on damaged grapes and crushing of the fruit facilitates the release of the fermentable sugars [39,40]. Obtaining fermentable sugars for beer and sake is quite different.…”

Section: Introductionmentioning

confidence: 99%

Saccharomyces arboricola and Its Hybrids’ Propensity for Sake Production: Interspecific Hybrids Reveal Increased Fermentation Abilities and a Mosaic Metabolic Profile

et al. 2020

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The use of interspecific hybrids during the industrial fermentation process has been well established, positioning the frontier of advancement in brewing to capitalize on the potential of Saccharomyces hybridization. Interspecific yeast hybrids used in modern monoculture inoculations benefit from a wide range of volatile metabolites that broaden the organoleptic complexity. This is the first report of sake brewing by Saccharomyces arboricola and its hybrids. S. arboricola x S. cerevisiae direct-mating generated cryotolerant interspecific hybrids which increased yields of ethanol and ethyl hexanoate compared to parental strains, important flavor attributes of fine Japanese ginjo sake rice wine. Hierarchical clustering heatmapping with principal component analysis for metabolic profiling was used in finding low levels of endogenous amino/organic acids clustered S. arboricola apart from the S. cerevisiae industrial strains. In sake fermentations, hybrid strains showed a mosaic profile of parental strains, while metabolic analysis suggested S. arboricola had a lower amino acid net uptake than S. cerevisiae. Additionally, this research found an increase in ethanolic fermentation from pyruvate and increased sulfur metabolism. Together, these results suggest S. arboricola is poised for in-depth metabolomic exploration in sake fermentation.

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Gene Expression in Yeasts During Wine Fermentation

Cited by 6 publications

References 208 publications

Saccharomyces cerevisiaegene expression during fermentation of Pinot noir wines at industrially relevant scale

Saccharomyces cerevisiaegene expression during fermentation of Pinot noir wines at industrially relevant scale

Mapping global shifts inSaccharomyces cerevisiaegene expression across asynchronous time trajectories with diffusion maps

Saccharomyces arboricola and Its Hybrids’ Propensity for Sake Production: Interspecific Hybrids Reveal Increased Fermentation Abilities and a Mosaic Metabolic Profile

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